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Seeing Into the Brain

Video of 20130422 3-D analysis of intact mouse hippocampus

CLARITY provided this 3D view showing a thick slice of a mouse brain’s memory hub, or hippocampus. It reveals a few different types of cells: projecting neurons (green), connecting interneurons (red), and layers of support cells, or glia (blue). Conventional 2D methods require that brain tissue be thinly sliced, sacrificing the ability to analyze such intact components in relation to each other. CLARITY permits such typing of molecular and cellular components to be performed repeatedly in the same brain. Source: Karl Deisseroth, Stanford University

Researchers developed a technique that preserves the brain’s 3-D structure down to the molecular level. The accomplishment allows study of the brain’s inner workings at a scale never before possible.

Scientists seeking to understand the brain’s fine structure and connections have been faced with tradeoffs. To gain access to deeply buried structures and reach a high enough resolution to study cells, molecules and genes, they had to cut brain tissue into extremely thin sections. This deforms the tissue. The approach also makes it difficult to address broader questions about brain wiring and circuitry.

A team at Stanford University led by Drs. Kwanghun Chung and Karl Deisseroth aimed to transform human brain tissue into a stable, intact and accessible form that could be used for structural and molecular studies. They saw opportunity in the fact that the fats, or lipids, that make up the membranes enclosing cells block chemical probes and light. They set out to replace the lipids with something clear and permeable that would also hold everything else in place. Their work was funded in part by an NIH Director’s Award and NIH’s National Institute of Mental Health (NIMH).

The team began by infusing a mixture containing compounds that link molecules together. When heated, the mixture forms a clear, porous gel (a “hydrogel”) that holds the brain’s tissue in place. At this point, not only are molecules linked to each other within the tissue; the hydrogel is also linked to biomolecules, including proteins, nucleic acids and small molecules.

Lipids are removed from this structure by applying a gentle electric field. Lipids that have no links to the gel migrate out of the tissue, leaving the rest of the crosslinked molecules intact. The result is a brain transformed for analysis. The method, called Clear Lipid-exchanged Anatomically Rigid Imaging/immunostaining-compatible Tissue hYdrogel (CLARITY), was described online in Nature on April 10, 2013.

The researchers showed that CLARITY outperformed conventional methods across a range of previously problematic technical challenges. The scientists were able to view the entire “clarified” brain of a mouse genetically engineered to express a fluorescent protein. They showed that antibodies and other probes could readily travel through clarified brains to mark specific molecules and cell structures, such as proteins embedded in cell membranes and individual nerve fibers.

Probes were readily added and removed from clarified brains, leaving tissue available for multiple rounds of analysis with different probes. In addition, the researchers showed they could subsequently analyze clarified brain tissue with an electron microscope to resolve ultrafine structure.

The scientists used CLARITY to analyze a postmortem brain of a person with autism. Even though the brain had been stored for 6 years, the researchers could trace individual nerve fibers and cells.

“CLARITY has the potential to unmask fine details of brains from people with brain disorders without losing larger scale circuit perspective,” says NIH Director Dr. Francis S. Collins. The method could also potentially be used to study other organs.